Figure 4.

Relationships between RNA structure and protein domain organization. (A) Median SHAPE reactivities over 75‐nucleotide windows, which provide a metric for overall RNA structure, for the 5′ end of the HIV‐1 genome [82]. (B) Low SHAPE reactivities, reflecting higher levels of RNA structure, correlate with unstructured protein linkers in the gag polyprotein. Interdomain linkers (green) and the intra‐domain loops (yellow) are illustrated between the independently folding domains of gag (blue, red, pink, and grey structures). (C) PARS scores averaged over 3000 yeast mRNAs for 5′ UTR (green), coding region (blue), and 3′ UTR (red) regions [100].